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nanonext - Lightweight Toolkit for Messaging, Concurrency and the Web

R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. A toolkit for messaging, concurrency and the web. High-performance socket messaging over in-process, IPC, TCP, WebSocket and secure TLS transports implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and survey. A threaded concurrency framework with intuitive 'aio' objects that resolve automatically upon completion of asynchronous operations, and synchronisation primitives that allow R to wait on events signalled by concurrent threads. A unified HTTP server hosting REST endpoints, WebSocket connections and streaming on a single port, with a built-in HTTP client.

Last updated

mbedtls

11.01 score 172 dependents 92 scripts 53k downloads

Rduckhts - 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API <https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.

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bamduckdb-extensionfastqhtslibvcf

6.88 score 19 stars 2 dependents 37 scripts 355 downloads

Rducks - Register R User-Defined Functions in DuckDB

R package and 'DuckDB' extension bridge for registering R functions as 'DuckDB' user-defined functions (UDFs). The package is designed around a loaded 'DuckDB' extension, declarative type descriptors, direct native vector marshalling, and explicit execution discipline for safe interaction with R from 'DuckDB' execution. The inter-process worker transport uses vendored 'NNG' (nanomsg next generation).

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cduckdb-extension

5.82 score 9 stars 27 scripts

Ropendal - Abstract Filesystem Access for R via 'Apache OpenDAL'

Provides a byte-oriented abstract filesystem interface for R backed by the Rust crate of 'Apache OpenDAL' <https://opendal.apache.org/>. The package is designed around filesystem primitives, asynchronous Aio-like operations inspired by 'nanonext', pluggable raw-vector serializers, and a native C API for direct async byte access by other R packages.

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filesystemopendalrustcargo

5.45 score 5 stars 25 scripts

Rfmalloc - Out-of-Core Arrays with Pluggable Codecs and Compute Backends

Computes on arrays that do not fit in memory. Vectors, matrices and tensors are allocated inside a memory-mapped file through R's ALTREP interface, backed by a patched copy of the 'fmalloc' allocator, so available RAM becomes a speed gradient rather than a hard limit. Two plugin registries sit on that substrate: a codec registry deciding how bytes are stored, from lossless floating-point and sparse encodings to compressed and quantized blocks, and a matrix-multiply backend registry deciding how products are computed, defaulting to whatever 'BLAS' the R build links against. Matrix products stream in bounded panels and release the pages they have consumed, so operands larger than memory still multiply. A registered backend may decline any product, in which case the default path answers it, so results never depend on which backend is selected. Also provides persistent and scratch runtimes, durable reference-based serialization, explicit vector lifecycle management, multiple runtime handles per session, and out-of-core reductions and principal components for genomics-scale matrices.

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altrepblasgenomicsggmlggufllmllm-inferencemallocmemory-mappedmmapout-of-corequantizationsimdcpp

4.86 score 4 stars 4 dependents 43 scripts

RGlimpse2 - An 'R' Wrapper for 'GLIMPSE2' Low-Coverage Sequencing Imputation and Phasing

Builds the pinned in-tree 'GLIMPSE2' chromosome chunking, reference splitting, phasing and imputation, and ligation programs against the 'htslib' supplied by 'Rduckhts'. Stateless R functions invoke one packaged executable with explicit argument vectors and return typed results or typed operational errors. Pinned GRCh37 and GRCh38 genetic maps are installed for explicit offline lookup. The phasing executable is selected explicitly from portable and runtime-supported AVX2, AVX-512, or NEON builds without searching 'PATH'.

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ancestryglimpse2imputation

4.81 score

Rminibwa - Native R Bindings and SIMD Dispatch for 'minibwa'

Provides native R bindings to the 'minibwa' genomic read aligner with raw-vector query input, external-pointer alignment batches, ALTREP column views, and an installed C API for downstream packages. The package builds staged Single Instruction Multiple Data ('SIMD') KSW backends, selects portable scalar, SSE4, or AVX2 code at runtime without global instruction-set compiler flags, and on native platforms links to the exact 'htslib' build supplied by 'Rduckhts' as its alignment-format dependency.

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alignmentaltrepbioinformaticsc-apigenomicsminibwasimdzlib

4.08 score 5 scripts

Rggml - Vendored 'GGML' Tensor Library with C-Callable Compute API

Vendors the core, official 'GGUF' implementation, and CPU backend of the 'GGML' tensor library (<https://github.com/ggml-org/ggml>) as a static library and exposes its core tensor-context and matrix-multiply compute path through 'R_RegisterCCallable' C-callable entry points. This is a carrier package: it has no high-level R modeling API of its own. Other R packages link to it ('LinkingTo') to build and compute 'GGML' tensor graphs (including quantized types such as Q4_K) from their own C or C++ code without re-vendoring 'GGML'. The CPU backend is always built. Native targets also build the BLAS backend for dense products; webR uses the CPU backend because its Fortran ABI differs. The 'Vulkan' and NVIDIA 'CUDA' backends are independent opt-in builds.

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altrepblasgenomicsggmlggufllmllm-inferencemallocmemory-mappedmmapout-of-corequantizationsimdopenblascpp

4.00 score 4 stars 2 dependents 12 scripts

RClinVarbitration - Build Tidy ClinVar Evidence and Arbitration Tables

Joins official 'ClinVar' variant and submission reports directly into one tidy scalar 'DuckDB' table containing variations, alleles, GRCh37/GRCh38 locations, decisions, source assertions, and gene links. ClinVarbitration policy is implemented in SQL over those reports. An optional package-owned native extension streams VCV XML into the same table when richer observations, conditions, citations, attributes, and attributable evidence text are required, and streams PubMed baseline or update XML into scalar PMID-authoritative literature relations.

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bioinformaticsclinvarduckdbgenomics

3.88 score 8 scripts

Rgguf - Official GGUF Parsing and Typed Storage Views

Reads 'GGUF' model files, the file format used by the 'llama.cpp' project (<https://github.com/ggerganov/llama.cpp>) to store large language model tensors and metadata. Tensors can be decoded into file-backed 'Rfmalloc' arrays, copied at their native codec density, or borrowed as zero-copy read-only spans over the original model mapping. Parsing, writing, and quantized decoding use the official 'GGML' GGUF implementation exposed by the sibling 'Rggml' package. Metadata key-value pairs and the tensor directory are exposed as ordinary R lists and data frames. A minimal writer is included to create 'GGUF' files containing 32-bit floating point tensors, primarily to support round-trip testing.

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altrepblasgenomicsggmlggufllmllm-inferencemallocmemory-mappedmmapout-of-corequantizationsimd

3.70 score 4 stars 1 dependents 12 scripts

CanardAbsurd - Checkpointed R Workflows over 'DuckDB' and 'Quack'

Runs durable R tasks using 'DuckDB' for state and the 'Quack' extension for remote Structured Query Language (SQL) access. Provides database hosting, leased task claims, checkpoint replay, retries, durable sleeps, and a pull-based R worker. External side effects require application-level idempotency.

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duckdbdurable-executionquackslop

3.60 score 1 stars

Rllm - Native Quantized Matrix Products and LLM Inference over 'Rfmalloc' Tensors

The composition layer of the 'Rfmalloc' ecosystem: it registers 'Rggml' (a vendored 'GGML' build with runtime-SIMD-dispatched quantized kernels) as a codec-aware matrix-multiply backend for 'Rfmalloc', so that products of file-backed, quantized tensors run natively in quantized space (weights stay 'Q4_K'/'Q6_K'/... encoded, activations are quantized on the fly) instead of being decoded to double first. Combined with 'Rgguf', which exposes 'GGUF' model weights as borrowed typed spans, this lets a larger-than-memory model's linear layers be multiplied through 'GGML's SIMD-accelerated dot kernels zero-copy from the original model mapping. Typed semantic programs written through an R module-and-pipe architecture language describe llama, Qwen3.5, LFM2MoE, EmbeddingGemma, ESM-2, OpenSpliceAI, Evo 2 and Tiny Recursive Models. Bound programs join those serializable graphs to mapped parameter storage. Implemented lowerings provide persistent state, pooled embeddings, byte-level generation, and CPU or optional CUDA execution; a reference interpreter executes the same dataflow through explicit R operator tables and structured recurrence.

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altrepblasgenomicsggmlggufllmllm-inferencemallocmemory-mappedmmapout-of-corequantizationsimd

3.54 score 4 stars 25 scripts

RBCFTools - Bundled 'FastDup', 'Samtools', 'BCFtools', and 'HTSlib' Utilities

Bundles patched 'FastDup', 'Samtools', and 'BCFtools' command-line executables together with the 'HTSlib' and 'libbcftools' libraries for reading and manipulating VCF, BCF, SAM, BAM, and CRAM files. All bundled executables are built against one shared vendored 'HTSlib' source. Provides shell-free pipelines for composing bundled or external executables. Also provides streaming facilities from VCF and BCF to Apache Arrow via 'nanoarrow', export to Arrow IPC and Parquet via 'duckdb', a native 'bcf_reader' extension, and utilities for reading and writing VCF and BCF data in 'DuckLake'.

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bcftoolsduckdbducklakegenomicshtslibnanoarrowparquet

3.44 score 2 stars 25 scripts

Rzarrs - R Bindings to 'zarrs': Zarr V3 Storage for Multidimensional Arrays

R bindings to the 'zarrs' Rust library <https://github.com/zarrs/zarrs> for reading Zarr V3 (and compatible Zarr V2) stores from local disk, HTTP/HTTPS, and S3 by default, with optional GCS and Azure Blob support at source-install time. Supports local '.zarr.zip' VCF Zarr archives, multiple codecs (gzip, zstd, sharding), and the common numeric data types. SIMD-accelerated codec paths are selected automatically at runtime by the underlying Rust dependency crates.

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rustzarrzarrscargo

3.32 score 6 stars 9 scripts

Rduckvep - DuckDB Variant Consequence Annotation

Builds and loads the bundled DuckVEP C extension for relation-first variant consequence and phased-haplotype annotation.

Last updated

3.23 score 2 stars

Rpgen - PLINK 2 Genotype Ingestion into File-Backed Storage

Uses the 'PLINK 2' pgenlib library and its native importers (<https://github.com/chrchang/plink-ng>) to ingest PGEN, PLINK 1 BED, PED/MAP, TPED/TFAM, VCF/BCF, BGEN, Oxford GEN, HAPS/legend, EIGENSTRAT, and legacy dosage sources into bounded, file-backed 'Rfmalloc' layouts. Hardcalls, dosages, and phase are transferred as typed record panels, allowing the destination to choose a packed codec or full-precision storage without constructing a complete R matrix. The vendored native readers are also exposed through 'R_RegisterCCallable' for sibling packages.

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altrepblasgenomicsggmlggufllmllm-inferencemallocmemory-mappedmmapout-of-corequantizationsimdlibzstdlibdeflatezlib

3.15 score 4 stars 9 scripts

RfmallocStatgen - Statistical Genetics on Rfmalloc Genotype Tensors

Runs genome-scale statistical genetics methods over Rfmalloc's file-backed, compressed genotype tensors ('bed' at 2 bits per genotype, 'dosage' at 1 byte per genotype), closing over the analysis stack popularized by 'bigsnpr' and 'bigstatsr' on denser storage with native readers, and adding haplotype methods that a genotype-only stack cannot express. Methods are implemented from published algorithms and validated against 'bigsnpr' and 'bigstatsr' as numerical oracles. The exception is the randomized-SVD workhorse, which is pinned from GPL-3 'PCAone' (Li 2023) with a deterministic dependency trim and R-console adaptation. The current surface includes streamed univariate regression and principal components, banded linkage disequilibrium, LDpred2, and an all-pairs colocalisation expressed as a single matrix multiply over any registered compute backend.

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altrepblasgenomicsggmlggufllmllm-inferencemallocmemory-mappedmmapout-of-corequantizationsimdcpp

3.15 score 4 stars 6 scripts

ducksemantics - DuckDB-Native Semantic and Retrieval Relations

DuckDB-native ontology graphs, validated Human Phenotype Ontology (HPO) observations, typed release-cataloged Monarch relations including read-only projections of attached dated packs, provider/snapshot-catalog-bound literature retrieval, and source-grounded semantic judgments. Bulk values are ordinary relations; optional S7 protocols are reserved for real prompt, embedding, parser, and annotator providers. The package does not store ClinVar or PubMed source data, download Monarch packs, rank cases, or evaluate benchmarks.

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2.88 score 3 stars 3 scripts

Rtskit - Native Access to Succinct Tree Sequences

Provides a native R interface to the 'tskit' C API for loading, inspecting, traversing, and writing succinct tree sequences. Tree sequences remain owned by native external pointers while typed R functions expose selected tables, opaque metadata, tree intervals, and declared source-population ancestry without a Python runtime.

Last updated

2.70 score

Rbebelm - Native 'BebeLM', 'EmbeddingGemma', and 'ColBERT' CPU Backends for R

Provides focused R interfaces to the pure-Rust 'BebeLM' CPU inference library <https://github.com/maximecb/bebelm> and a native pure-Rust implementation of the retrieval-trained 'EmbeddingGemma' encoder <https://ai.google.dev/gemma/docs/embeddinggemma>, and a native profile for LiquidAI's retrieval-trained LFM2.5-'ColBERT' GGUF encoder. The package exposes GGUF model loading, tokenizer access, semantic text embeddings, late-interaction token vectors and MaxSim scoring, streaming generation events, persistent conversation agents, 'BebeLM' tool-call parsing, R tool dispatch, and Rust-thread async generation jobs. Loaded agents share model weights in process through Rust reference-counted handles, and GGUF files are mapped read-only so repeated loads of the same file can share physical pages through the operating-system page cache. Native libraries are built as runtime-selected CPU backends so portable R binaries can use scalar code by default and optimized SIMD backends when available.

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local-llmrustsimdcargo

2.68 score 1 stars 16 scripts

Rdragmap - An 'R' Wrapper for Portable 'DRAGMAP' Short-Read Alignment

Builds the pinned in-tree 'DRAGMAP' hash-table generator and short-read aligner with a portable baseline and runtime-gated AVX2 on supported x86 processors. Stateless R functions build reference indexes and align FASTQ input through one package-owned executable without searching 'PATH'. The same source also compiles for AArch64, where 'SIMDe' maps the imported 128-bit vector operations to NEON.

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allignmentbioinformatics

2.60 score

rho - Asynchronous R Agent and Bioinformatics Substrate

Defines asynchronous tasks, streams, HTTP and provider protocols, agent and extension runtimes, compute and transport backends, coding tools, graphics artifacts, and declared bioinformatics resources in one package.

Last updated

2.40 score 1 stars

Rducksassy - Approximate String Matching for 'DuckDB'

Builds and loads the 'ducksassy' extension for 'DuckDB', providing approximate DNA, IUPAC and ASCII string matching through the 'Sassy' SIMD kernels. Search scalar values, pattern panels and CRISPR guide targets from SQL. The matching method is described by Beeloo and Groot Koerkamp (2026) <doi:10.1093/bioinformatics/btag244>.

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duckdb-extensionsassysimdstring-matchingrustcargo

2.18 score

XCNV - Copy Number Variant Annotation and Transparent Scoring

Provides bedtools-free copy-number-variant annotation, a portable evaluator and bundled runtime-neutral form of the published X-CNV model of Zhang et al. (2021), and independently authored, provenance-first scoring under the ACMG and ClinGen 2019 constitutional copy-number-variant standard. Large scientific annotation resources remain outside the package payload.

Last updated

cnvrare-diseasexcnv

2.00 score